This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Peptide modification by PTM or by mutation of amino acids is important to researcher in many fields. Phosphorilation in signaling and oxidation in protein damage are examples. These modifications affect protein structure and reactivity and can be used to study protein structures if induced artificially. In many cases the exact nature of the modification is not known or there are too many of them to consider using a protein database search program. A general program for discovering any kind of modification was written. It is based on 2D correlation of product-ion spectra to theoretical spectra or to existing spectra of unmodified peptides. A viewer for correlation analysis and locating the modification position is used.